meshi.energy.pairwiseNonBondedTerms.LennardJones
Class LennardJonesEnergyElement

java.lang.Object
  meshi.energy.EnergyElement
      meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyElement
          meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement

public class LennardJonesEnergyElement
extends NonBondedEnergyElement

Field Summary

static double	ALPHA
protected Atom	atom1
protected int	atom1Number
protected Atom	atom2
protected int	atom2Number
protected double	breakEnergy
protected double	breakEnergy4
protected double	breakEnergySquare4
protected double	contact
protected double	dCdD
protected double	dCdX
protected double	dCdY
protected double	dCdZ
protected double	dEdD
protected double	dEdX
protected double	dEdY
protected double	dEdZ
private Distance	distance
protected DistanceMatrix	distanceMatrix
protected double	energy
protected double	epsilon
private int	FIRST
protected boolean	frozen
static double	MAX_ENERGY
protected double	maxEnergy
protected double	minusTwelveSigma6
protected static double[][][]	parameters
protected double	rMax
private int	SECOND
protected double	sigma
protected double	sigma6
protected double	sigma6EpsilonFour
protected double	weight

Fields inherited from class meshi.energy.EnergyElement

atoms, dFormatSrt, dFormatStd, DX, relativeDiffTolerance, VERY_SMALL, XYZ

Constructor Summary

LennardJonesEnergyElement()

LennardJonesEnergyElement(DistanceMatrix distanceMatrix, double weight, double[][][] parameters)

Method Summary

double	contact()
double	contact(double weight)
double	contactAtoms(double weight)
double	dEdXAtom(int index)
double	dEdYAtom(int index)
double	dEdZAtom(int index)
double	distance()
double	evaluate()
double	getDEdD()
double	getDEdX()
double	getDEdY()
double	getDEdZ()
void	set(java.lang.Object obj)
protected void	setAtoms()
java.lang.String	toString()
void	updateAtoms()
double	updateEnergy()

Methods inherited from class meshi.energy.EnergyElement

atoms, evaluateAtoms, frozen, test, updateFrozen

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

MAX_ENERGY

public static final double MAX_ENERGY

See Also:

Constant Field Values

ALPHA

public static final double ALPHA

See Also:

Constant Field Values

distanceMatrix

protected DistanceMatrix distanceMatrix

atom1

protected Atom atom1

atom2

protected Atom atom2

atom1Number

protected int atom1Number

atom2Number

protected int atom2Number

epsilon

protected double epsilon

sigma

protected double sigma

sigma6

protected double sigma6

sigma6EpsilonFour

protected double sigma6EpsilonFour

minusTwelveSigma6

protected double minusTwelveSigma6

frozen

protected boolean frozen

dEdD

protected double dEdD

dEdX

protected double dEdX

dEdY

protected double dEdY

dEdZ

protected double dEdZ

energy

protected double energy

weight

protected double weight

maxEnergy

protected double maxEnergy

breakEnergy

protected double breakEnergy

breakEnergy4

protected double breakEnergy4

breakEnergySquare4

protected double breakEnergySquare4

rMax

protected double rMax

contact

protected double contact

dCdD

protected double dCdD

dCdX

protected double dCdX

dCdY

protected double dCdY

dCdZ

protected double dCdZ

FIRST

private final int FIRST

See Also:

Constant Field Values

SECOND

private final int SECOND

See Also:

Constant Field Values

distance

private Distance distance

parameters

protected static double[][][] parameters

Constructor Detail

LennardJonesEnergyElement

public LennardJonesEnergyElement()

LennardJonesEnergyElement

public LennardJonesEnergyElement(DistanceMatrix distanceMatrix,
                                 double weight,
                                 double[][][] parameters)

Method Detail

setAtoms

protected void setAtoms()

Specified by:

setAtoms in class EnergyElement

distance

public double distance()

set

public void set(java.lang.Object obj)

Specified by:

set in class NonBondedEnergyElement

evaluate

public double evaluate()

Specified by:

evaluate in class EnergyElement

updateEnergy

public double updateEnergy()

updateAtoms

public void updateAtoms()

contactAtoms

public double contactAtoms(double weight)

dEdXAtom

public double dEdXAtom(int index)

dEdYAtom

public double dEdYAtom(int index)

dEdZAtom

public double dEdZAtom(int index)

contact

public double contact(double weight)

contact

public double contact()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getDEdD

public final double getDEdD()

Returns:

Returns the dEdD.

getDEdX

public final double getDEdX()

Returns:

Returns the dEdX.

getDEdY

public final double getDEdY()

Returns:

Returns the dEdY.

getDEdZ

public final double getDEdZ()

Returns:

Returns the dEdZ.